Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/c256cb4d9dc92b9928e5943b36bd46/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/3d7658213dd56fa2e7013e06745507/fi_workdir/aih-tih-sc-55b175-R1_A23WJ53LT4_1.gtf Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/c256cb4d9dc92b9928e5943b36bd46/.command.run ==> STAGING COMPLETE (3 inputs) Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/agat_config.yaml file ------------------------------------------------------------------------------ | Another GFF Analysis Toolkit (AGAT) - Version: v1.2.0 | | https://github.com/NBISweden/AGAT | | National Bioinformatics Infrastructure Sweden (NBIS) - www.nbis.se | ------------------------------------------------------------------------------ ------ Start parsing ------ -------------------------- parse options and metadata -------------------------- => Accessing the feature_levels YAML file Using standard /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/feature_levels.yaml file => Attribute used to group features when no Parent/ID relationship exists (i.e common tag): * locus_tag * gene_id => merge_loci option deactivated => Machine information: This script is being run by perl v5.32.1 Bioperl location being used: /usr/local/lib/perl5/site_perl/Bio/ Operating system being used: linux => Accessing Ontology No ontology accessible from the gff file header! We use the SOFA ontology distributed with AGAT: /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo Read ontology /usr/local/lib/perl5/site_perl/auto/share/dist/AGAT/so.obo: 4 root terms, and 2596 total terms, and 1516 leaf terms Filtering ontology: We found 1861 terms that are sequence_feature or is_a child of it. --------------------------------- parsing file --------------------------------- => Number of line in file: 2007 => Number of comment lines: 0 => Fasta included: No => Number of features lines: 2007 => Number of feature type (3rd column): 2 * Level1: 0 => * level2: 0 => * level3: 2 => exon CDS * unknown: 0 => =>Check because only level3 features: * Number of feature with Parent attribute:0 * Number of feature with a common attribute:2007 => Some common attributes and some Parent attributes missing. /!\ For features where both are missing A single Level2 features (e.g. mRNA) and a single level1 (e.g. gene) will be created by AGAT, and all level3 feautres (e,g, CDS,exon) will be attached to them. This is probably not what you want... see B. 2.2 and 3. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html /!\ For features where the common attribute or the parent attribute is missing, it would be fine as long as you do not expect isoforms in your annotation (Eukaryote). see B. 4. at https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html !! You might try to fix the issue by choosing a common tag attribute to use in order to group the features correctly (parameter --ct in agat_convert_sp_gxf2gxf.pl). => Version of the Bioperl GFF parser selected by AGAT: 2 ------ End parsing (done in 1 second) ------ ------ Start checks ------ ---------------------------- Check1: feature types ----------------------------- ----------------------------------- ontology ----------------------------------- All feature types in agreement with the Ontology. ------------------------------------- agat ------------------------------------- AGAT can deal with all the encountered feature types (3rd column) ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check2: duplicates ------------------------------ None found ------------------------------ done in 0 seconds ------------------------------- -------------------------- Check3: sequential bucket --------------------------- Nothing to check as sequential bucket! ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check4: l2 linked to l3 ---------------------------- L1 and L2 created: AC092807.3--DDAH1 HAVANA gene 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding AC092807.3--DDAH1 HAVANA mRNA 13647 23704 . + . FI_gene_label "DDAH1^ENSG00000153904.21" ; ID "AC092807.3--DDAH1^ENST00000284031.13" ; Parent "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; ccdsid "CCDS705.1" ; exon_id "ENSE00001013010.7" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^DDAH1^ENSG00000153904.21" ; gene_name DDAH1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000191181.3" ; havana_transcript "OTTHUMT00000029189.3" ; hgnc_id "HGNC:2715" ; level 2 ; orig_coord_info "chr1,85464743,85465045,-" ; protein_id "ENSP00000284031.8" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "AC092807.3--DDAH1^ENST00000284031.13" ; transcript_name "DDAH1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: FBXO25--AC240565.1 HAVANA gene 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding FBXO25--AC240565.1 HAVANA mRNA 2640 15007 . + . FI_gene_label "FBXO25^ENSG00000147364.17" ; ID "FBXO25--AC240565.1^ENST00000276326.9" ; Parent "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; ccdsid "CCDS5954.1" ; exon_id "ENSE00003460930.1" ; exon_number 2 ; gene_id "FBXO25--AC240565.1^FBXO25^ENSG00000147364.17" ; gene_name FBXO25 ; gene_type protein_coding ; havana_gene "OTTHUMG00000090341.8" ; havana_transcript "OTTHUMT00000206713.2" ; hgnc_id "HGNC:13596" ; level 2 ; orig_coord_info "chr8,431358,431444,+" ; protein_id "ENSP00000276326.6" ; tag basic CCDS ; transcript_id "FBXO25--AC240565.1^ENST00000276326.9" ; transcript_name "FBXO25-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 7417 15704 . + . FI_gene_label "KLRK1^ENSG00000213809.9" ; ID "KLRC4--KLRK1^ENST00000240618.11" ; Parent "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; ccdsid "CCDS8623.1" ; exon_id "ENSE00003640305.1" ; exon_number 2 ; gene_id "KLRC4--KLRK1^KLRK1^ENSG00000213809.9" ; gene_name KLRK1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168574.3" ; havana_transcript "OTTHUMT00000400269.2" ; hgnc_id "HGNC:18788" ; level 2 ; orig_coord_info "chr12,10388771,10388810,-" ; protein_id "ENSP00000240618.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000240618.11" ; transcript_name "KLRK1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: KLRC4--KLRK1 HAVANA gene 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding KLRC4--KLRK1 HAVANA mRNA 1001 3376 . + . FI_gene_label "KLRC4^ENSG00000183542.5" ; ID "KLRC4--KLRK1^ENST00000309384.2" ; Parent "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; ccdsid "CCDS8624.1" ; exon_id "ENSE00001145174.1" ; exon_number 1 ; gene_id "KLRC4--KLRK1^KLRC4^ENSG00000183542.5" ; gene_name KLRC4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000168575.2" ; havana_transcript "OTTHUMT00000400108.2" ; hgnc_id "HGNC:6377" ; level 2 ; orig_coord_info "chr12,10409389,10409575,-" ; protein_id "ENSP00000310216.1" ; tag basic appris_principal_1 CCDS ; transcript_id "KLRC4--KLRK1^ENST00000309384.2" ; transcript_name "KLRC4-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NOP58--KIAA2012 HAVANA gene 1028 16793 . + . FI_gene_label "NOP58^ENSG00000055044.11" ; ID "NOP58--KIAA2012^NOP58^ENSG00000055044.11" ; ccdsid "CCDS2353.1" ; exon_id "ENSE00001828228.2" ; exon_number 1 ; gene_id "NOP58--KIAA2012^NOP58^ENSG00000055044.11" ; gene_name NOP58 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132840.4" ; havana_transcript "OTTHUMT00000256313.3" ; hgnc_id "HGNC:29926" ; level 2 ; orig_coord_info "chr2,202265942,202265986,+" ; protein_id "ENSP00000264279.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NOP58--KIAA2012^ENST00000264279.10" ; transcript_name "NOP58-201" ; transcript_support_level 1 ; transcript_type protein_coding NOP58--KIAA2012 HAVANA mRNA 1028 16793 . + . FI_gene_label "NOP58^ENSG00000055044.11" ; ID "NOP58--KIAA2012^ENST00000264279.10" ; Parent "NOP58--KIAA2012^NOP58^ENSG00000055044.11" ; ccdsid "CCDS2353.1" ; exon_id "ENSE00001828228.2" ; exon_number 1 ; gene_id "NOP58--KIAA2012^NOP58^ENSG00000055044.11" ; gene_name NOP58 ; gene_type protein_coding ; havana_gene "OTTHUMG00000132840.4" ; havana_transcript "OTTHUMT00000256313.3" ; hgnc_id "HGNC:29926" ; level 2 ; orig_coord_info "chr2,202265942,202265986,+" ; protein_id "ENSP00000264279.5" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "NOP58--KIAA2012^ENST00000264279.10" ; transcript_name "NOP58-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: NOP58--KIAA2012 HAVANA gene 19828 31475 . + . FI_gene_label "KIAA2012^ENSG00000182329.14" ; ID "NOP58--KIAA2012^KIAA2012^ENSG00000182329.14" ; exon_id "ENSE00002260502.1" ; exon_number 1 ; gene_id "NOP58--KIAA2012^KIAA2012^ENSG00000182329.14" ; gene_name KIAA2012 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154580.7" ; havana_transcript "OTTHUMT00000336162.2" ; hgnc_id "HGNC:51250" ; level 2 ; orig_coord_info "chr2,202073628,202073711,+" ; protein_id "ENSP00000490419.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "NOP58--KIAA2012^ENST00000459709.5" ; transcript_name "KIAA2012-202" ; transcript_support_level 2 ; transcript_type protein_coding NOP58--KIAA2012 HAVANA mRNA 19828 31475 . + . FI_gene_label "KIAA2012^ENSG00000182329.14" ; ID "NOP58--KIAA2012^ENST00000459709.5" ; Parent "NOP58--KIAA2012^KIAA2012^ENSG00000182329.14" ; exon_id "ENSE00002260502.1" ; exon_number 1 ; gene_id "NOP58--KIAA2012^KIAA2012^ENSG00000182329.14" ; gene_name KIAA2012 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154580.7" ; havana_transcript "OTTHUMT00000336162.2" ; hgnc_id "HGNC:51250" ; level 2 ; orig_coord_info "chr2,202073628,202073711,+" ; protein_id "ENSP00000490419.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "NOP58--KIAA2012^ENST00000459709.5" ; transcript_name "KIAA2012-202" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: PEX14--AC079054.1 HAVANA gene 2294 14084 . + . FI_gene_label "PEX14^ENSG00000142655.13" ; ID "PEX14--AC079054.1^PEX14^ENSG00000142655.13" ; ccdsid "CCDS30582.1" ; exon_id "ENSE00001472556.4" ; exon_number 1 ; gene_id "PEX14--AC079054.1^PEX14^ENSG00000142655.13" ; gene_name PEX14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001908.3" ; havana_transcript "OTTHUMT00000005414.2" ; hgnc_id "HGNC:8856" ; level 2 ; orig_coord_info "chr1,10474967,10475002,+" ; protein_id "ENSP00000349016.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PEX14--AC079054.1^ENST00000356607.9" ; transcript_name "PEX14-201" ; transcript_support_level 1 ; transcript_type protein_coding PEX14--AC079054.1 HAVANA mRNA 2294 14084 . + . FI_gene_label "PEX14^ENSG00000142655.13" ; ID "PEX14--AC079054.1^ENST00000356607.9" ; Parent "PEX14--AC079054.1^PEX14^ENSG00000142655.13" ; ccdsid "CCDS30582.1" ; exon_id "ENSE00001472556.4" ; exon_number 1 ; gene_id "PEX14--AC079054.1^PEX14^ENSG00000142655.13" ; gene_name PEX14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001908.3" ; havana_transcript "OTTHUMT00000005414.2" ; hgnc_id "HGNC:8856" ; level 2 ; orig_coord_info "chr1,10474967,10475002,+" ; protein_id "ENSP00000349016.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PEX14--AC079054.1^ENST00000356607.9" ; transcript_name "PEX14-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PEX14--RN7SKP159 HAVANA gene 2294 14084 . + . FI_gene_label "PEX14^ENSG00000142655.13" ; ID "PEX14--RN7SKP159^PEX14^ENSG00000142655.13" ; ccdsid "CCDS30582.1" ; exon_id "ENSE00001472556.4" ; exon_number 1 ; gene_id "PEX14--RN7SKP159^PEX14^ENSG00000142655.13" ; gene_name PEX14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001908.3" ; havana_transcript "OTTHUMT00000005414.2" ; hgnc_id "HGNC:8856" ; level 2 ; orig_coord_info "chr1,10474967,10475002,+" ; protein_id "ENSP00000349016.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PEX14--RN7SKP159^ENST00000356607.9" ; transcript_name "PEX14-201" ; transcript_support_level 1 ; transcript_type protein_coding PEX14--RN7SKP159 HAVANA mRNA 2294 14084 . + . FI_gene_label "PEX14^ENSG00000142655.13" ; ID "PEX14--RN7SKP159^ENST00000356607.9" ; Parent "PEX14--RN7SKP159^PEX14^ENSG00000142655.13" ; ccdsid "CCDS30582.1" ; exon_id "ENSE00001472556.4" ; exon_number 1 ; gene_id "PEX14--RN7SKP159^PEX14^ENSG00000142655.13" ; gene_name PEX14 ; gene_type protein_coding ; havana_gene "OTTHUMG00000001908.3" ; havana_transcript "OTTHUMT00000005414.2" ; hgnc_id "HGNC:8856" ; level 2 ; orig_coord_info "chr1,10474967,10475002,+" ; protein_id "ENSP00000349016.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PEX14--RN7SKP159^ENST00000356607.9" ; transcript_name "PEX14-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: PMS2P6--CCDC146 HAVANA gene 9058 29425 . + . FI_gene_label "CCDC146^ENSG00000135205.15" ; ID "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; ccdsid "CCDS34671.1" ; exon_id "ENSE00003536120.1" ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3" ; havana_transcript "OTTHUMT00000341449.2" ; hgnc_id "HGNC:29296" ; level 2 ; orig_coord_info "chr7,77167669,77167824,+" ; protein_id "ENSP00000285871.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5" ; transcript_name "CCDC146-201" ; transcript_support_level 1 ; transcript_type protein_coding PMS2P6--CCDC146 HAVANA mRNA 9058 29425 . + . FI_gene_label "CCDC146^ENSG00000135205.15" ; ID "PMS2P6--CCDC146^ENST00000285871.5" ; Parent "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; ccdsid "CCDS34671.1" ; exon_id "ENSE00003536120.1" ; exon_number 2 ; gene_id "PMS2P6--CCDC146^CCDC146^ENSG00000135205.15" ; gene_name CCDC146 ; gene_type protein_coding ; havana_gene "OTTHUMG00000162595.3" ; havana_transcript "OTTHUMT00000341449.2" ; hgnc_id "HGNC:29296" ; level 2 ; orig_coord_info "chr7,77167669,77167824,+" ; protein_id "ENSP00000285871.4" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "PMS2P6--CCDC146^ENST00000285871.5" ; transcript_name "CCDC146-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RIC3--ALDH1A1 HAVANA gene 22211 36609 . + . FI_gene_label "ALDH1A1^ENSG00000165092.13" ; ID "RIC3--ALDH1A1^ALDH1A1^ENSG00000165092.13" ; ccdsid "CCDS6644.1" ; exon_id "ENSE00001876240.2" ; exon_number 1 ; gene_id "RIC3--ALDH1A1^ALDH1A1^ENSG00000165092.13" ; gene_name ALDH1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020019.3" ; havana_transcript "OTTHUMT00000052679.2" ; hgnc_id "HGNC:402" ; level 2 ; orig_coord_info "chr9,72952935,72953000,-" ; protein_id "ENSP00000297785.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RIC3--ALDH1A1^ENST00000297785.8" ; transcript_name "ALDH1A1-201" ; transcript_support_level 1 ; transcript_type protein_coding RIC3--ALDH1A1 HAVANA mRNA 22211 36609 . + . FI_gene_label "ALDH1A1^ENSG00000165092.13" ; ID "RIC3--ALDH1A1^ENST00000297785.8" ; Parent "RIC3--ALDH1A1^ALDH1A1^ENSG00000165092.13" ; ccdsid "CCDS6644.1" ; exon_id "ENSE00001876240.2" ; exon_number 1 ; gene_id "RIC3--ALDH1A1^ALDH1A1^ENSG00000165092.13" ; gene_name ALDH1A1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000020019.3" ; havana_transcript "OTTHUMT00000052679.2" ; hgnc_id "HGNC:402" ; level 2 ; orig_coord_info "chr9,72952935,72953000,-" ; protein_id "ENSP00000297785.3" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RIC3--ALDH1A1^ENST00000297785.8" ; transcript_name "ALDH1A1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RIC3--ALDH1A1 HAVANA gene 1031 15769 . + . FI_gene_label "RIC3^ENSG00000166405.15" ; ID "RIC3--ALDH1A1^RIC3^ENSG00000166405.15" ; ccdsid "CCDS55742.1" ; exon_id "ENSE00003848333.1" ; exon_number 1 ; gene_id "RIC3--ALDH1A1^RIC3^ENSG00000166405.15" ; gene_name RIC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165694.6" ; havana_transcript "OTTHUMT00000385900.3" ; hgnc_id "HGNC:30338" ; level 2 ; orig_coord_info "chr11,8168866,8168989,-" ; protein_id "ENSP00000308820.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "RIC3--ALDH1A1^ENST00000309737.11" ; transcript_name "RIC3-201" ; transcript_support_level 1 ; transcript_type protein_coding RIC3--ALDH1A1 HAVANA mRNA 1031 15769 . + . FI_gene_label "RIC3^ENSG00000166405.15" ; ID "RIC3--ALDH1A1^ENST00000309737.11" ; Parent "RIC3--ALDH1A1^RIC3^ENSG00000166405.15" ; ccdsid "CCDS55742.1" ; exon_id "ENSE00003848333.1" ; exon_number 1 ; gene_id "RIC3--ALDH1A1^RIC3^ENSG00000166405.15" ; gene_name RIC3 ; gene_type protein_coding ; havana_gene "OTTHUMG00000165694.6" ; havana_transcript "OTTHUMT00000385900.3" ; hgnc_id "HGNC:30338" ; level 2 ; orig_coord_info "chr11,8168866,8168989,-" ; protein_id "ENSP00000308820.6" ; tag basic MANE_Select appris_alternative_1 CCDS ; transcript_id "RIC3--ALDH1A1^ENST00000309737.11" ; transcript_name "RIC3-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RN7SL753P--KIAA2012 HAVANA gene 4325 15972 . + . FI_gene_label "KIAA2012^ENSG00000182329.14" ; ID "RN7SL753P--KIAA2012^KIAA2012^ENSG00000182329.14" ; exon_id "ENSE00002260502.1" ; exon_number 1 ; gene_id "RN7SL753P--KIAA2012^KIAA2012^ENSG00000182329.14" ; gene_name KIAA2012 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154580.7" ; havana_transcript "OTTHUMT00000336162.2" ; hgnc_id "HGNC:51250" ; level 2 ; orig_coord_info "chr2,202073628,202073711,+" ; protein_id "ENSP00000490419.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "RN7SL753P--KIAA2012^ENST00000459709.5" ; transcript_name "KIAA2012-202" ; transcript_support_level 2 ; transcript_type protein_coding RN7SL753P--KIAA2012 HAVANA mRNA 4325 15972 . + . FI_gene_label "KIAA2012^ENSG00000182329.14" ; ID "RN7SL753P--KIAA2012^ENST00000459709.5" ; Parent "RN7SL753P--KIAA2012^KIAA2012^ENSG00000182329.14" ; exon_id "ENSE00002260502.1" ; exon_number 1 ; gene_id "RN7SL753P--KIAA2012^KIAA2012^ENSG00000182329.14" ; gene_name KIAA2012 ; gene_type protein_coding ; havana_gene "OTTHUMG00000154580.7" ; havana_transcript "OTTHUMT00000336162.2" ; hgnc_id "HGNC:51250" ; level 2 ; orig_coord_info "chr2,202073628,202073711,+" ; protein_id "ENSP00000490419.1" ; tag mRNA_end_NF cds_end_NF ; transcript_id "RN7SL753P--KIAA2012^ENST00000459709.5" ; transcript_name "KIAA2012-202" ; transcript_support_level 2 ; transcript_type protein_coding L1 and L2 created: RNASE10--CD38 HAVANA gene 6254 19390 . + . FI_gene_label "CD38^ENSG00000004468.13" ; ID "RNASE10--CD38^CD38^ENSG00000004468.13" ; ccdsid "CCDS3417.1" ; exon_id "ENSE00001131145.4" ; exon_number 1 ; gene_id "RNASE10--CD38^CD38^ENSG00000004468.13" ; gene_name CD38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048206.6" ; havana_transcript "OTTHUMT00000250322.3" ; hgnc_id "HGNC:1667" ; level 2 ; orig_coord_info "chr4,15778415,15778647,+" ; protein_id "ENSP00000226279.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNASE10--CD38^ENST00000226279.8" ; transcript_name "CD38-201" ; transcript_support_level 1 ; transcript_type protein_coding RNASE10--CD38 HAVANA mRNA 6254 19390 . + . FI_gene_label "CD38^ENSG00000004468.13" ; ID "RNASE10--CD38^ENST00000226279.8" ; Parent "RNASE10--CD38^CD38^ENSG00000004468.13" ; ccdsid "CCDS3417.1" ; exon_id "ENSE00001131145.4" ; exon_number 1 ; gene_id "RNASE10--CD38^CD38^ENSG00000004468.13" ; gene_name CD38 ; gene_type protein_coding ; havana_gene "OTTHUMG00000048206.6" ; havana_transcript "OTTHUMT00000250322.3" ; hgnc_id "HGNC:1667" ; level 2 ; orig_coord_info "chr4,15778415,15778647,+" ; protein_id "ENSP00000226279.2" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "RNASE10--CD38^ENST00000226279.8" ; transcript_name "CD38-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: RNASE10--CD38 HAVANA gene 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--CD38^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding RNASE10--CD38 HAVANA mRNA 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--CD38^ENST00000328444.5" ; Parent "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--CD38^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--CD38^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: RNASE10--STON2 HAVANA gene 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--STON2^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding RNASE10--STON2 HAVANA mRNA 2484 3200 . + . FI_gene_label "RNASE10^ENSG00000182545.6" ; ID "RNASE10--STON2^ENST00000328444.5" ; Parent "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; ccdsid "CCDS32035.1" ; exon_id "ENSE00001299018.5" ; exon_number 1 ; gene_id "RNASE10--STON2^RNASE10^ENSG00000182545.6" ; gene_name RNASE10 ; gene_type protein_coding ; havana_gene "OTTHUMG00000170986.1" ; havana_transcript "OTTHUMT00000411088.1" ; hgnc_id "HGNC:19275" ; level 2 ; orig_coord_info "chr14,20510472,20511119,+" ; protein_id "ENSP00000333358.5" ; tag basic appris_principal_4 CCDS ; transcript_id "RNASE10--STON2^ENST00000328444.5" ; transcript_name "RNASE10-201" ; transcript_support_level NA ; transcript_type protein_coding L1 and L2 created: RNASE10--STON2 HAVANA gene 19313 23270 . + . FI_gene_label "STON2^ENSG00000140022.13" ; ID "RNASE10--STON2^STON2^ENSG00000140022.13" ; exon_id "ENSE00002458916.2" ; exon_number 1 ; gene_id "RNASE10--STON2^STON2^ENSG00000140022.13" ; gene_name STON2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171416.6" ; havana_transcript "OTTHUMT00000413315.2" ; hgnc_id "HGNC:30652" ; level 1 ; orig_coord_info "chr14,81276901,81276998,-" ; protein_id "ENSP00000450577.2" ; tag RNA_Seq_supported_partial mRNA_start_NF cds_start_NF exp_conf ; transcript_id "RNASE10--STON2^ENST00000553821.2" ; transcript_name "STON2-201" ; transcript_support_level 3 ; transcript_type protein_coding RNASE10--STON2 HAVANA mRNA 19313 23270 . + . FI_gene_label "STON2^ENSG00000140022.13" ; ID "RNASE10--STON2^ENST00000553821.2" ; Parent "RNASE10--STON2^STON2^ENSG00000140022.13" ; exon_id "ENSE00002458916.2" ; exon_number 1 ; gene_id "RNASE10--STON2^STON2^ENSG00000140022.13" ; gene_name STON2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000171416.6" ; havana_transcript "OTTHUMT00000413315.2" ; hgnc_id "HGNC:30652" ; level 1 ; orig_coord_info "chr14,81276901,81276998,-" ; protein_id "ENSP00000450577.2" ; tag RNA_Seq_supported_partial mRNA_start_NF cds_start_NF exp_conf ; transcript_id "RNASE10--STON2^ENST00000553821.2" ; transcript_name "STON2-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 1021 7754 . + . FI_gene_label "STX16^ENSG00000124222.22" ; ID "STX16--NPEPL1^ENST00000312283.12" ; Parent "STX16--NPEPL1^STX16^ENSG00000124222.22" ; exon_id "ENSE00003459479.1" ; exon_number 3 ; gene_id "STX16--NPEPL1^STX16^ENSG00000124222.22" ; gene_name STX16 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033084.8" ; havana_transcript "OTTHUMT00000267911.2" ; hgnc_id "HGNC:11431" ; level 2 ; orig_coord_info "chr20,58667505,58667597,+" ; protein_id "ENSP00000312086.8" ; tag alternative_5_UTR mRNA_end_NF cds_end_NF ; transcript_id "STX16--NPEPL1^ENST00000312283.12" ; transcript_name "STX16-201" ; transcript_support_level 3 ; transcript_type protein_coding L1 and L2 created: STX16--NPEPL1 HAVANA gene 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding STX16--NPEPL1 HAVANA mRNA 18353 29399 . + . FI_gene_label "NPEPL1^ENSG00000215440.12" ; ID "STX16--NPEPL1^ENST00000356091.11" ; Parent "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; ccdsid "CCDS46621.1" ; exon_id "ENSE00001408052.7" ; exon_number 1 ; gene_id "STX16--NPEPL1^NPEPL1^ENSG00000215440.12" ; gene_name NPEPL1 ; gene_type protein_coding ; havana_gene "OTTHUMG00000033060.8" ; havana_transcript "OTTHUMT00000080402.7" ; hgnc_id "HGNC:16244" ; level 2 ; orig_coord_info "chr20,58692901,58693050,+" ; protein_id "ENSP00000348395.6" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "STX16--NPEPL1^ENST00000356091.11" ; transcript_name "NPEPL1-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--AC240565.1 HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--AC240565.1 HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--AC240565.1^ENST00000326270.13" ; Parent "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--AC240565.1^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--AC240565.1^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TLK2--FAM157A HAVANA gene 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding TLK2--FAM157A HAVANA mRNA 4784 35054 . + . FI_gene_label "TLK2^ENSG00000146872.18" ; ID "TLK2--FAM157A^ENST00000326270.13" ; Parent "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; ccdsid "CCDS62283.1" ; exon_id "ENSE00003568961.1" ; exon_number 2 ; gene_id "TLK2--FAM157A^TLK2^ENSG00000146872.18" ; gene_name TLK2 ; gene_type protein_coding ; havana_gene "OTTHUMG00000179176.3" ; havana_transcript "OTTHUMT00000445140.1" ; hgnc_id "HGNC:11842" ; level 2 ; orig_coord_info "chr17,62481126,62481206,+" ; protein_id "ENSP00000316512.9" ; tag basic CCDS ; transcript_id "TLK2--FAM157A^ENST00000326270.13" ; transcript_name "TLK2-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 1052 15760 . + . FI_gene_label "TVP23C^ENSG00000175106.17" ; ID "TVP23C--CDRT4^ENST00000225576.7" ; Parent "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; ccdsid "CCDS11170.1" ; exon_id "ENSE00001105678.2" ; exon_number 1 ; gene_id "TVP23C--CDRT4^TVP23C^ENSG00000175106.17" ; gene_name TVP23C ; gene_type protein_coding ; havana_gene "OTTHUMG00000171461.10" ; havana_transcript "OTTHUMT00000130705.3" ; hgnc_id "HGNC:30453" ; level 2 ; orig_coord_info "chr17,15563437,15563448,-" ; protein_id "ENSP00000225576.3" ; tag basic CCDS ; transcript_id "TVP23C--CDRT4^ENST00000225576.7" ; transcript_name "TVP23C-201" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: TVP23C--CDRT4 HAVANA gene 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding TVP23C--CDRT4 HAVANA mRNA 19889 25887 . + . FI_gene_label "CDRT4^ENSG00000239704.11" ; ID "TVP23C--CDRT4^ENST00000619038.5" ; Parent "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; ccdsid "CCDS73995.1" ; exon_id "ENSE00003735347.1" ; exon_number 3 ; gene_id "TVP23C--CDRT4^CDRT4^ENSG00000239704.11" ; gene_name CDRT4 ; gene_type protein_coding ; havana_gene "OTTHUMG00000059070.14" ; havana_transcript "OTTHUMT00000130383.9" ; hgnc_id "HGNC:14383" ; level 2 ; orig_coord_info "chr17,15440208,15440238,-" ; protein_id "ENSP00000482523.1" ; tag basic MANE_Select appris_principal_1 CCDS ; transcript_id "TVP23C--CDRT4^ENST00000619038.5" ; transcript_name "CDRT4-204" ; transcript_support_level 1 ; transcript_type protein_coding L1 and L2 created: AC092807.3--DDAH1 HAVANA gene 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA AC092807.3--DDAH1 HAVANA RNA 1101 8302 . + . FI_gene_label "AC092807.3^ENSG00000282057.1" ; ID "AC092807.3--DDAH1^ENST00000467530.5" ; Parent "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; exon_id "ENSE00001891111.1" ; exon_number 1 ; gene_id "AC092807.3--DDAH1^AC092807.3^ENSG00000282057.1" ; gene_name "AC092807.3" ; gene_type lncRNA ; havana_gene "OTTHUMG00000010578.6" ; havana_transcript "OTTHUMT00000029193.2" ; level 2 ; orig_coord_info "chr1,85577984,85578150,-" ; tag basic ; transcript_id "AC092807.3--DDAH1^ENST00000467530.5" ; transcript_name "AC092807.3-203" ; transcript_support_level 2 ; transcript_type lncRNA L1 and L2 created: FBXO25--AC240565.1 HAVANA gene 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA FBXO25--AC240565.1 HAVANA RNA 26102 34357 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "FBXO25--AC240565.1^ENST00000624936.2" ; Parent "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "FBXO25--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "FBXO25--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: PEX14--AC079054.1 HAVANA gene 17085 17626 . + . FI_gene_label "AC079054.1^ENSG00000253189.1" ; ID "PEX14--AC079054.1^AC079054.1^ENSG00000253189.1" ; exon_id "ENSE00002107239.1" ; exon_number 1 ; gene_id "PEX14--AC079054.1^AC079054.1^ENSG00000253189.1" ; gene_name "AC079054.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163615.1" ; havana_transcript "OTTHUMT00000374527.1" ; level 2 ; orig_coord_info "chr8,6036850,6036974,-" ; tag basic ; transcript_id "PEX14--AC079054.1^ENST00000523090.1" ; transcript_name "AC079054.1-201" ; transcript_support_level 3 ; transcript_type lncRNA PEX14--AC079054.1 HAVANA RNA 17085 17626 . + . FI_gene_label "AC079054.1^ENSG00000253189.1" ; ID "PEX14--AC079054.1^ENST00000523090.1" ; Parent "PEX14--AC079054.1^AC079054.1^ENSG00000253189.1" ; exon_id "ENSE00002107239.1" ; exon_number 1 ; gene_id "PEX14--AC079054.1^AC079054.1^ENSG00000253189.1" ; gene_name "AC079054.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000163615.1" ; havana_transcript "OTTHUMT00000374527.1" ; level 2 ; orig_coord_info "chr8,6036850,6036974,-" ; tag basic ; transcript_id "PEX14--AC079054.1^ENST00000523090.1" ; transcript_name "AC079054.1-201" ; transcript_support_level 3 ; transcript_type lncRNA L1 and L2 created: PEX14--RN7SKP159 ENSEMBL gene 17085 17376 . + . FI_gene_label "RN7SKP159^ENSG00000222589.1" ; ID "PEX14--RN7SKP159^RN7SKP159^ENSG00000222589.1" ; exon_id "ENSE00001590475.1" ; exon_number 1 ; gene_id "PEX14--RN7SKP159^RN7SKP159^ENSG00000222589.1" ; gene_name RN7SKP159 ; gene_type misc_RNA ; hgnc_id "HGNC:45883" ; level 3 ; orig_coord_info "chr8,5910945,5911236,-" ; tag basic ; transcript_id "PEX14--RN7SKP159^ENST00000410657.1" ; transcript_name "RN7SKP159-201" ; transcript_support_level NA ; transcript_type misc_RNA PEX14--RN7SKP159 ENSEMBL RNA 17085 17376 . + . FI_gene_label "RN7SKP159^ENSG00000222589.1" ; ID "PEX14--RN7SKP159^ENST00000410657.1" ; Parent "PEX14--RN7SKP159^RN7SKP159^ENSG00000222589.1" ; exon_id "ENSE00001590475.1" ; exon_number 1 ; gene_id "PEX14--RN7SKP159^RN7SKP159^ENSG00000222589.1" ; gene_name RN7SKP159 ; gene_type misc_RNA ; hgnc_id "HGNC:45883" ; level 3 ; orig_coord_info "chr8,5910945,5911236,-" ; tag basic ; transcript_id "PEX14--RN7SKP159^ENST00000410657.1" ; transcript_name "RN7SKP159-201" ; transcript_support_level NA ; transcript_type misc_RNA L1 and L2 created: PMS2P12--AC004980.4 HAVANA gene 1001 2551 . + . FI_gene_label "PMS2P12^ENSG00000228546.2" ; ID "PMS2P12--AC004980.4^PMS2P12^ENSG00000228546.2" ; exon_id "ENSE00002491666.1" ; exon_number 1 ; gene_id "PMS2P12--AC004980.4^PMS2P12^ENSG00000228546.2" ; gene_name PMS2P12 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157128.1" ; havana_transcript "OTTHUMT00000347531.1" ; hgnc_id "HGNC:13641" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,102337316,102337402,+" ; tag basic ; transcript_id "PMS2P12--AC004980.4^ENST00000432573.1" ; transcript_name "PMS2P12-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene PMS2P12--AC004980.4 HAVANA RNA 1001 2551 . + . FI_gene_label "PMS2P12^ENSG00000228546.2" ; ID "PMS2P12--AC004980.4^ENST00000432573.1" ; Parent "PMS2P12--AC004980.4^PMS2P12^ENSG00000228546.2" ; exon_id "ENSE00002491666.1" ; exon_number 1 ; gene_id "PMS2P12--AC004980.4^PMS2P12^ENSG00000228546.2" ; gene_name PMS2P12 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157128.1" ; havana_transcript "OTTHUMT00000347531.1" ; hgnc_id "HGNC:13641" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,102337316,102337402,+" ; tag basic ; transcript_id "PMS2P12--AC004980.4^ENST00000432573.1" ; transcript_name "PMS2P12-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene L1 and L2 created: PMS2P12--AC004980.4 HAVANA gene 5552 6015 . + . FI_gene_label "AC004980.4^ENSG00000250778.1" ; ID "PMS2P12--AC004980.4^AC004980.4^ENSG00000250778.1" ; exon_id "ENSE00002460193.1" ; exon_number 1 ; gene_id "PMS2P12--AC004980.4^AC004980.4^ENSG00000250778.1" ; gene_name "AC004980.4" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155723.2" ; havana_transcript "OTTHUMT00000341392.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,76521611,76521677,+" ; tag basic ; transcript_id "PMS2P12--AC004980.4^ENST00000513375.1" ; transcript_name "AC004980.4-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene PMS2P12--AC004980.4 HAVANA RNA 5552 6015 . + . FI_gene_label "AC004980.4^ENSG00000250778.1" ; ID "PMS2P12--AC004980.4^ENST00000513375.1" ; Parent "PMS2P12--AC004980.4^AC004980.4^ENSG00000250778.1" ; exon_id "ENSE00002460193.1" ; exon_number 1 ; gene_id "PMS2P12--AC004980.4^AC004980.4^ENSG00000250778.1" ; gene_name "AC004980.4" ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000155723.2" ; havana_transcript "OTTHUMT00000341392.2" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,76521611,76521677,+" ; tag basic ; transcript_id "PMS2P12--AC004980.4^ENST00000513375.1" ; transcript_name "AC004980.4-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene L1 and L2 created: PMS2P6--CCDC146 HAVANA gene 1001 5876 . + . FI_gene_label "PMS2P6^ENSG00000174384.9" ; ID "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; exon_id "ENSE00002441642.1" ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2" ; havana_transcript "OTTHUMT00000347345.2" ; hgnc_id "HGNC:33514" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,73093657,73093796,+" ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5" ; transcript_name "PMS2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene PMS2P6--CCDC146 HAVANA RNA 1001 5876 . + . FI_gene_label "PMS2P6^ENSG00000174384.9" ; ID "PMS2P6--CCDC146^ENST00000333674.5" ; Parent "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; exon_id "ENSE00002441642.1" ; exon_number 1 ; gene_id "PMS2P6--CCDC146^PMS2P6^ENSG00000174384.9" ; gene_name PMS2P6 ; gene_type unprocessed_pseudogene ; havana_gene "OTTHUMG00000157066.2" ; havana_transcript "OTTHUMT00000347345.2" ; hgnc_id "HGNC:33514" ; level 2 ; ont "PGO:0000005" ; orig_coord_info "chr7,73093657,73093796,+" ; tag basic ; transcript_id "PMS2P6--CCDC146^ENST00000333674.5" ; transcript_name "PMS2P6-201" ; transcript_support_level NA ; transcript_type unprocessed_pseudogene L1 and L2 created: RN7SL753P--KIAA2012 ENSEMBL gene 1001 1290 . + . FI_gene_label "RN7SL753P^ENSG00000264275.1" ; ID "RN7SL753P--KIAA2012^RN7SL753P^ENSG00000264275.1" ; exon_id "ENSE00002710697.1" ; exon_number 1 ; gene_id "RN7SL753P--KIAA2012^RN7SL753P^ENSG00000264275.1" ; gene_name RN7SL753P ; gene_type misc_RNA ; hgnc_id "HGNC:46769" ; level 3 ; orig_coord_info "chr2,202333439,202333728,+" ; tag basic ; transcript_id "RN7SL753P--KIAA2012^ENST00000581238.1" ; transcript_name "RN7SL753P-201" ; transcript_support_level NA ; transcript_type misc_RNA RN7SL753P--KIAA2012 ENSEMBL RNA 1001 1290 . + . FI_gene_label "RN7SL753P^ENSG00000264275.1" ; ID "RN7SL753P--KIAA2012^ENST00000581238.1" ; Parent "RN7SL753P--KIAA2012^RN7SL753P^ENSG00000264275.1" ; exon_id "ENSE00002710697.1" ; exon_number 1 ; gene_id "RN7SL753P--KIAA2012^RN7SL753P^ENSG00000264275.1" ; gene_name RN7SL753P ; gene_type misc_RNA ; hgnc_id "HGNC:46769" ; level 3 ; orig_coord_info "chr2,202333439,202333728,+" ; tag basic ; transcript_id "RN7SL753P--KIAA2012^ENST00000581238.1" ; transcript_name "RN7SL753P-201" ; transcript_support_level NA ; transcript_type misc_RNA L1 and L2 created: TLK2--AC240565.1 HAVANA gene 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA TLK2--AC240565.1 HAVANA RNA 40046 48301 . + . FI_gene_label "AC240565.1^ENSG00000280136.2" ; ID "TLK2--AC240565.1^ENST00000624936.2" ; Parent "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; exon_id "ENSE00003756821.1" ; exon_number 1 ; gene_id "TLK2--AC240565.1^AC240565.1^ENSG00000280136.2" ; gene_name "AC240565.1" ; gene_type lncRNA ; havana_gene "OTTHUMG00000189256.2" ; havana_transcript "OTTHUMT00000479189.2" ; level 2 ; orig_coord_info "chr17,118383,118578,-" ; tag not_best_in_genome_evidence basic ; transcript_id "TLK2--AC240565.1^ENST00000624936.2" ; transcript_name "AC240565.1-201" ; transcript_support_level 5 ; transcript_type lncRNA L1 and L2 created: TLK2--FAM157A HAVANA gene 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript TLK2--FAM157A HAVANA RNA 40046 44186 . + . FI_gene_label "FAM157A^ENSG00000236438.7" ; ID "TLK2--FAM157A^ENST00000437428.3" ; Parent "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; exon_id "ENSE00002579345.3" ; exon_number 1 ; gene_id "TLK2--FAM157A^FAM157A^ENSG00000236438.7" ; gene_name FAM157A ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000187506.3" ; havana_transcript "OTTHUMT00000488453.1" ; hgnc_id "HGNC:34079" ; level 2 ; orig_coord_info "chr3,198153287,198153409,+" ; tag basic ; transcript_id "TLK2--FAM157A^ENST00000437428.3" ; transcript_name "FAM157A-201" ; transcript_support_level 3 ; transcript_type processed_transcript L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene TLK2P1--AC110079.1 HAVANA RNA 1001 4192 . + . FI_gene_label "TLK2P1^ENSG00000226049.3" ; ID "TLK2P1--AC110079.1^ENST00000530992.1" ; Parent "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; exon_id "ENSE00002174619.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^TLK2P1^ENSG00000226049.3" ; gene_name TLK2P1 ; gene_type processed_pseudogene ; havana_gene "OTTHUMG00000166422.1" ; havana_transcript "OTTHUMT00000389700.1" ; hgnc_id "HGNC:18048" ; level 1 ; ont "PGO:0000004" ; orig_coord_info "chr17,34036681,34039872,-" ; tag pseudo_consens basic ; transcript_id "TLK2P1--AC110079.1^ENST00000530992.1" ; transcript_name "TLK2P1-201" ; transcript_support_level NA ; transcript_type processed_pseudogene L1 and L2 created: TLK2P1--AC110079.1 HAVANA gene 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript TLK2P1--AC110079.1 HAVANA RNA 7193 19707 . + . FI_gene_label "AC110079.1^ENSG00000260404.3" ; ID "TLK2P1--AC110079.1^ENST00000567913.2" ; Parent "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; exon_id "ENSE00002625896.1" ; exon_number 1 ; gene_id "TLK2P1--AC110079.1^AC110079.1^ENSG00000260404.3" ; gene_name "AC110079.1" ; gene_type transcribed_unprocessed_pseudogene ; havana_gene "OTTHUMG00000161164.4" ; havana_transcript "OTTHUMT00000364170.2" ; level 2 ; orig_coord_info "chr4,118591773,118591895,+" ; tag dotter_confirmed basic ; transcript_id "TLK2P1--AC110079.1^ENST00000567913.2" ; transcript_name "AC110079.1-201" ; transcript_support_level 5 ; transcript_type processed_transcript 188 cases fixed where L3 features have parent feature(s) missing ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check5: l1 linked to l2 ---------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- --------------------------- Check6: remove orphan l1 --------------------------- We remove only those not supposed to be orphan None found ------------------------------ done in 0 seconds ------------------------------- ------------------------- Check7: all level3 locations ------------------------- ------------------------------ done in 0 seconds ------------------------------- ------------------------------ Check8: check cds ------------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- ----------------------------- Check9: check exons ------------------------------ No exons created No exons locations modified No supernumerary exons removed No level2 locations modified ------------------------------ done in 0 seconds ------------------------------- ----------------------------- Check10: check utrs ------------------------------ 303 UTRs created that were missing No UTRs locations modified No supernumerary UTRs removed ------------------------------ done in 0 seconds ------------------------------- ------------------------ Check11: all level2 locations ------------------------- No problem found ------------------------------ done in 0 seconds ------------------------------- ------------------------ Check12: all level1 locations ------------------------- We fixed 22 wrong level1 location cases ------------------------------ done in 0 seconds ------------------------------- ---------------------- Check13: remove identical isoforms ---------------------- None found ------------------------------ done in 0 seconds ------------------------------- ------ End checks (done in 0 second) ------ GFF3 file parsed